Query         gi|254780452|ref|YP_003064865.1| hypothetical protein CLIBASIA_01685 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 259
No_of_seqs    135 out of 1134
Neff          7.3 
Searched_HMMs 13730
Date          Wed Jun  1 05:02:31 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780452.hhm -d /home/congqian_1/database/scop/scop70_1_75.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 d3cx5e2 f.23.12.1 (E:31-86) Ir   8.1      38  0.0028    9.7   1.9   10   30-39     22-31  (56)
  2 d1irqa_ a.43.1.4 (A:) Omega tr   6.6      50  0.0036    8.9   2.2   19   14-32     25-43  (48)
  3 d1ppje2 f.23.12.1 (E:1-69) Iro   6.5      51  0.0037    8.9   4.4   34    2-39      8-41  (69)
  4 d2r7ga2 a.74.1.3 (A:644-785) R   5.7      60  0.0043    8.4   2.9   19   23-41      2-20  (142)
  5 d1v2za_ a.186.1.1 (A:) Circadi   5.4      64  0.0047    8.2   1.8   26    6-31     24-49  (106)
  6 d1r8ja1 a.186.1.1 (A:177-282)    5.4      64  0.0047    8.2   1.7   14   17-30     32-45  (106)
  7 d1r5qa_ a.186.1.1 (A:) Circadi   5.1      69   0.005    8.0   1.5   27    5-31     13-39  (98)
  8 d2dt5a1 a.4.5.38 (A:4-77) Tran   5.0      70  0.0051    8.0   1.2   13  157-169    40-52  (74)
  9 d1jkwa2 a.74.1.1 (A:162-287) C   4.8      74  0.0054    7.8   3.0   35  116-150    29-63  (126)
 10 d1i27a_ a.4.5.30 (A:) C-termin   4.8      75  0.0054    7.8   1.3   11   21-31     11-21  (73)

No 1  
>d3cx5e2 f.23.12.1 (E:31-86) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
Probab=8.06  E-value=38  Score=9.70  Aligned_cols=10  Identities=30%  Similarity=0.534  Sum_probs=6.0

Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254780452|r   30 IRVYNLMALG   39 (259)
Q Consensus        30 ~kVY~~la~~   39 (259)
                      ||+|+++-+|
T Consensus        22 ~r~fsY~mvG   31 (56)
T d3cx5e2          22 GRSYAYFMVG   31 (56)
T ss_dssp             HHHHHHHHHH
T ss_pred             CCEEEEEEEE
T ss_conf             5467887540


No 2  
>d1irqa_ a.43.1.4 (A:) Omega transcriptional repressor {Streptococcus pyogenes [TaxId: 1314]}
Probab=6.56  E-value=50  Score=8.95  Aligned_cols=19  Identities=26%  Similarity=0.543  Sum_probs=11.1

Q ss_pred             CCHHHHHHHHHHHHHHHHH
Q ss_conf             0002455669999999999
Q gi|254780452|r   14 GSGFGSTIDQGLRAYMIRV   32 (259)
Q Consensus        14 ~~~~~~~~d~~lr~Fi~kV   32 (259)
                      ++..-...|+.+|.++||+
T Consensus        25 ggnvkevm~~~l~~~~~~~   43 (48)
T d1irqa_          25 GGNVKEVMDQALEEYIRKY   43 (48)
T ss_dssp             TCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHH
T ss_conf             8889999999999999986


No 3  
>d1ppje2 f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Cow (Bos taurus) [TaxId: 9913]}
Probab=6.48  E-value=51  Score=8.90  Aligned_cols=34  Identities=18%  Similarity=0.226  Sum_probs=15.9

Q ss_pred             CHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             40145421023200024556699999999999999999
Q gi|254780452|r    2 SDIRNYQRVVNSGSGFGSTIDQGLRAYMIRVYNLMALG   39 (259)
Q Consensus         2 ~~~~n~~~~~~~~~~~~~~~d~~lr~Fi~kVY~~la~~   39 (259)
                      -|+.+|++.........+...+.-|    |+|+++-.+
T Consensus         8 PDFs~YRr~~~~d~~~~~~~s~~~R----k~fsYl~~g   41 (69)
T d1ppje2           8 PDFSDYRRPEVLDSTKSSKESSEAR----KGFSYLVTA   41 (69)
T ss_dssp             CCCTTTBCGGGCCTTSCSHHHHHHH----HHHHHHHHH
T ss_pred             CCCHHHCCCCCCCCCCCCCCCCCHH----CEEHHHHHH
T ss_conf             9944433543348531135574100----100134545


No 4  
>d2r7ga2 a.74.1.3 (A:644-785) Retinoblastoma tumor suppressor domains {Human (Homo sapiens) [TaxId: 9606]}
Probab=5.71  E-value=60  Score=8.45  Aligned_cols=19  Identities=32%  Similarity=0.501  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999
Q gi|254780452|r   23 QGLRAYMIRVYNLMALGLG   41 (259)
Q Consensus        23 ~~lr~Fi~kVY~~la~~L~   41 (259)
                      .+++-|.||||.+-+.-+-
T Consensus         2 tsl~iFfrKvy~La~~Rl~   20 (142)
T d2r7ga2           2 TSLSLFYKKVYRLAYLRLN   20 (142)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             2999999999999999999


No 5  
>d1v2za_ a.186.1.1 (A:) Circadian clock protein KaiA, C-terminal domain {Thermosynechococcus elongatus bp-1 [TaxId: 197221]}
Probab=5.38  E-value=64  Score=8.24  Aligned_cols=26  Identities=8%  Similarity=0.243  Sum_probs=9.5

Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             54210232000245566999999999
Q gi|254780452|r    6 NYQRVVNSGSGFGSTIDQGLRAYMIR   31 (259)
Q Consensus         6 n~~~~~~~~~~~~~~~d~~lr~Fi~k   31 (259)
                      +|+...-+--+.+.++++.+-+|+..
T Consensus        24 ~YR~IlLsYFs~d~~~nq~id~fVn~   49 (106)
T d1v2za_          24 IYRTIVLEYFNTDAKVNERIDEFVSK   49 (106)
T ss_dssp             HHHHHHHHTTCTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             99999999908957789999999999


No 6  
>d1r8ja1 a.186.1.1 (A:177-282) Circadian clock protein KaiA, C-terminal domain {Synechococcus elongatus PCC 7942 [TaxId: 1140]}
Probab=5.37  E-value=64  Score=8.23  Aligned_cols=14  Identities=14%  Similarity=0.323  Sum_probs=4.6

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             24556699999999
Q gi|254780452|r   17 FGSTIDQGLRAYMI   30 (259)
Q Consensus        17 ~~~~~d~~lr~Fi~   30 (259)
                      .+.++++.+-+|+.
T Consensus        32 ~d~~~nq~id~fVn   45 (106)
T d1r8ja1          32 PNSNLNQSIDNFVN   45 (106)
T ss_dssp             TTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             95788999999999


No 7  
>d1r5qa_ a.186.1.1 (A:) Circadian clock protein KaiA, C-terminal domain {Cyanobacterium (Nostoc sp. PCC 7120) [TaxId: 103690]}
Probab=5.09  E-value=69  Score=8.04  Aligned_cols=27  Identities=7%  Similarity=0.221  Sum_probs=10.6

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             454210232000245566999999999
Q gi|254780452|r    5 RNYQRVVNSGSGFGSTIDQGLRAYMIR   31 (259)
Q Consensus         5 ~n~~~~~~~~~~~~~~~d~~lr~Fi~k   31 (259)
                      ++|+...-+-.+.+.++++.+-+|+..
T Consensus        13 ~~YR~ill~YF~~~~~~nq~id~fVn~   39 (98)
T d1r5qa_          13 SDYRQILLSYFTTDKALKEKIDKFINA   39 (98)
T ss_dssp             HHHHHHHHHTTSCC--CHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             999999999918947789999999999


No 8  
>d2dt5a1 a.4.5.38 (A:4-77) Transcriptional repressor Rex, N-terminal domain {Thermus aquaticus [TaxId: 271]}
Probab=5.01  E-value=70  Score=7.98  Aligned_cols=13  Identities=31%  Similarity=0.805  Sum_probs=8.2

Q ss_pred             HHHHHHHHHHCCH
Q ss_conf             8655555542035
Q gi|254780452|r  157 YTTKRDLGPIGSF  169 (259)
Q Consensus       157 ~~tk~D~s~~g~~  169 (259)
                      .|-++||+..|.+
T Consensus        40 ~qVRKDls~fG~~   52 (74)
T d2dt5a1          40 FQVRKDLSYFGSY   52 (74)
T ss_dssp             HHHHHHHHHTTCC
T ss_pred             HHHHHHHHHHCCC
T ss_conf             9999879986578


No 9  
>d1jkwa2 a.74.1.1 (A:162-287) Cyclin H (mcs2) {Human (Homo sapiens) [TaxId: 9606]}
Probab=4.78  E-value=74  Score=7.82  Aligned_cols=35  Identities=26%  Similarity=0.321  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999987767899997421788999999999999
Q gi|254780452|r  116 LLYSALIGLSLSSFFLVYTSKSIVQTFFITAASFG  150 (259)
Q Consensus       116 ~~f~~~~G~tls~i~~~y~~~~I~~A~~~Ta~if~  150 (259)
                      .++..++--..+..+..|.|..|..|.+..+.--.
T Consensus        29 ~a~~~lnds~~Td~~l~y~P~qIalaal~~a~~~~   63 (126)
T d1jkwa2          29 TADDFLNRIALTDAYLLYTPSQIALTAILSSASRA   63 (126)
T ss_dssp             HHHHHHHHHTTSTHHHHSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCEEEEECHHHHHHHHHHHHHHHC
T ss_conf             99999999983781024078999999999988880


No 10 
>d1i27a_ a.4.5.30 (A:) C-terminal domain of the rap74 subunit of TFIIF {Human (Homo sapiens) [TaxId: 9606]}
Probab=4.77  E-value=75  Score=7.81  Aligned_cols=11  Identities=27%  Similarity=0.730  Sum_probs=5.7

Q ss_pred             HHHHHHHHHHH
Q ss_conf             66999999999
Q gi|254780452|r   21 IDQGLRAYMIR   31 (259)
Q Consensus        21 ~d~~lr~Fi~k   31 (259)
                      .++++|+|++|
T Consensus        11 tEeaVrRYL~R   21 (73)
T d1i27a_          11 TEDAVRRYLTR   21 (73)
T ss_dssp             CHHHHHHHHHH
T ss_pred             CHHHHHHHHHH
T ss_conf             89999999961


Done!